Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Drivers of decoupling and recoupling of crop and livestock systems at farm and territorial scales
    Garrett, Rachael D. ; Ryschawy, Julie ; Bell, Lindsay W. ; Cortner, Owen ; Ferreira, Joice ; Garik, Anna Victoria N. ; Gil, Juliana D.B. ; Klerkx, Laurens ; Moraine, Marc ; Peterson, Caitlin A. ; Reis, Júlio César Dos; Valentim, Judson F. - \ 2020
    Ecology and Society 25 (2020)1. - ISSN 1708-3087
    Innovation - Integrated crop livestock systems - Mixed farming systems - Socio-technical transitions - Sustainable agriculture - Technology adoption

    Crop and livestock production have become spatially decoupled in existing commercial agricultural regimes throughout the world. These segregated high input production systems contribute to some of the world’s most pressing sustainability challenges, including climate change, nutrient imbalances, water pollution, biodiversity decline, and increasingly precarious rural livelihoods. There is substantial evidence that by closing the loop in nutrient and energy cycles, recoupling crop and livestock systems at farm and territorial scales can help reduce the environmental externalities associated with conventional commercial farming without declines in profitability or yields. Yet such “integrated” crop and livestock systems remain rare as a proportion of global agricultural area. Based on an interdisciplinary workshop and additional literature review, we provide a comprehensive historical and international perspective on why integrated crop and livestock systems have declined in most regions and what conditions have fostered their persistence and reemergence in others. We also identify levers for encouraging the reemergence of integrated crop and livestock systems worldwide. We conclude that a major disruption of the current regime would be needed to foster crop-livestock reintegration, including a redesign of research programs, credit systems, payments for ecosystem services, insurance programs, and food safety regulations to focus on whole farm outcomes and the creation of a circular economy. An expansion of the number of integrated crop and livestock systems field trials and demonstrations and efforts to brand integrated crop and livestock systems as a form of sustainable agriculture through the development of eco-labels could also improve adoption, but would likely be unsuccessful at encouraging wide-scale change without a more radical transformation of the research and policy landscape.

    Social dimensions of fertility behavior and consumption patterns in the Anthropocene
    Barrett, Scott ; Dasgupta, Aisha ; Dasgupta, Partha ; Neil Adger, W. ; Anderies, John ; Bergh, Jeroen van den; Bledsoe, Caroline ; Bongaarts, John ; Carpenter, Stephen ; Stuart Chapin, F. ; Crépin, Anne Sophie ; Daily, Gretchen ; Ehrlich, Paul ; Folke, Carl ; Kautsky, Nils ; Lambin, Eric F. ; Levin, Simon A. ; Mäler, Karl Göran ; Naylor, Rosamond ; Nyborg, Karine ; Polasky, Stephen ; Scheffer, Marten ; Shogren, Jason ; Jørgensen, Peter Søgaard ; Walker, Brian ; Wilen, James - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)12. - ISSN 0027-8424 - p. 6300 - 6307.
    Consumption - Fertility - Socially embedded preferences

    We consider two aspects of the human enterprise that profoundly affect the global environment: population and consumption. We show that fertility and consumption behavior harbor a class of externalities that have not been much noted in the literature. Both are driven in part by attitudes and preferences that are not egoistic but socially embedded; that is, each household's decisions are influenced by the decisions made by others. In a famous paper, Garrett Hardin [G. Hardin, Science 162, 1243-1248 (1968)] drew attention to overpopulation and concluded that the solution lay in people “abandoning the freedom to breed.” That human attitudes and practices are socially embedded suggests that it is possible for people to reduce their fertility rates and consumption demands without experiencing a loss in wellbeing. We focus on fertility in sub-Saharan Africa and consumption in the rich world and argue that bottom-up social mechanisms rather than top-down government interventions are better placed to bring about those ecologically desirable changes.

    Assessing the sensitivity and repeatability of permanganate oxidizable carbon as a soil health metric: An interlab comparison across soils
    Wade, Jordon ; Maltais-Landry, Gabriel ; Lucas, Dawn E. ; Bongiorno, Giulia ; Bowles, Timothy M. ; Calderón, Francisco J. ; Culman, Steve W. ; Daughtridge, Rachel ; Ernakovich, Jessica G. ; Fonte, Steven J. ; Giang, Dinh ; Herman, Bethany L. ; Guan, Lindsey ; Jastrow, Julie D. ; Loh, Bryan H.H. ; Kelly, Courtland ; Mann, Meredith E. ; Matamala, Roser ; Miernicki, Elizabeth A. ; Peterson, Brandon ; Pulleman, Mirjam M. ; Scow, Kate M. ; Snapp, Sieglinde S. ; Thomas, Vanessa ; Tu, Xinyi ; Wang, Daoyuan ; Jelinski, Nicolas A. ; Liles, Garrett C. ; Barrios-Masias, Felipe H. ; Rippner, Devin A. ; Silveira, Maria L. ; Margenot, Andrew J. - \ 2020
    Geoderma 366 (2020). - ISSN 0016-7061

    Soil organic matter is central to the soil health framework. Therefore, reliable indicators of changes in soil organic matter are essential to inform land management decisions. Permanganate oxidizable carbon (POXC), an emerging soil health indicator, has shown promise for being sensitive to soil management. However, strict standardization is required for widespread implementation in research and commercial contexts. Here, we used 36 soils—three from each of the 12 USDA soil orders—to determine the effects of sieve size and soil mass of analysis on POXC results. Using replicated measurements across 12 labs in the US and the EU (n = 7951 samples), we quantified the relative importance of 1) variation between labs, 2) variation within labs, 3) effect soil mass, and 4) effect of soil sieve size on the repeatability of POXC. We found a wide range of overall variability in POXC values across labs (0.03 to 171.8%; mean = 13.4%), and much of this variability was attributable to within-lab variation (median = 6.5%) independently of soil mass or sieve size. Greater soil mass (2.5 g) decreased absolute POXC values by a mean of 177 mg kg−1 soil and decreased analytical variability by 6.5%. For soils with organic carbon (SOC) >10%, greater soil mass (2.5 g) resulted in more frequent POXC values above the limit of detection whereas the lower soil mass (0.75 g) resulted in POXC values below the limit of detection for SOC contents <5%. A finer sieve size increased absolute values of POXC by 124 mg kg−1 while decreasing the analytical variability by 1.8%. In general, soils with greater SOC contents had lower analytical variability. These results point to potential standardizations of the POXC protocol that can decrease the variability of the metric. We recommend that the POXC protocol be standardized to use 2.5 g for soils <10% SOC. Sieve size was a relatively small contributor to analytical variability and therefore we recommend that this decision be tailored to the study purpose. Tradeoffs associated with these standardizations can be mitigated, ultimately providing guidance on how to standardize POXC for routine analysis.

    Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants
    Makarova, Kira S. ; Wolf, Yuri I. ; Iranzo, Jaime ; Shmakov, Sergey A. ; Alkhnbashi, Omer S. ; Brouns, Stan J.J. ; Charpentier, Emmanuelle ; Cheng, David ; Haft, Daniel H. ; Horvath, Philippe ; Moineau, Sylvain ; Mojica, Francisco J.M. ; Scott, David ; Shah, Shiraz A. ; Siksnys, Virginijus ; Terns, Michael P. ; Venclovas, Česlovas ; White, Malcolm F. ; Yakunin, Alexander F. ; Yan, Winston ; Zhang, Feng ; Garrett, Roger A. ; Backofen, Rolf ; Oost, John van der; Barrangou, Rodolphe ; Koonin, Eugene V. - \ 2020
    Nature Reviews Microbiology 18 (2020). - ISSN 1740-1526 - p. 67 - 83.

    The number and diversity of known CRISPR–Cas systems have substantially increased in recent years. Here, we provide an updated evolutionary classification of CRISPR–Cas systems and cas genes, with an emphasis on the major developments that have occurred since the publication of the latest classification, in 2015. The new classification includes 2 classes, 6 types and 33 subtypes, compared with 5 types and 16 subtypes in 2015. A key development is the ongoing discovery of multiple, novel class 2 CRISPR–Cas systems, which now include 3 types and 17 subtypes. A second major novelty is the discovery of numerous derived CRISPR–Cas variants, often associated with mobile genetic elements that lack the nucleases required for interference. Some of these variants are involved in RNA-guided transposition, whereas others are predicted to perform functions distinct from adaptive immunity that remain to be characterized experimentally. The third highlight is the discovery of numerous families of ancillary CRISPR-linked genes, often implicated in signal transduction. Together, these findings substantially clarify the functional diversity and evolutionary history of CRISPR–Cas.

    Efficiency of insect-proof net tunnels in reducing virus-related seed degeneration in sweet potato
    Ogero, K.O. ; Kreuze, J.F. ; McEwan, M.A. ; Luambano, N.D. ; Bachwenkizi, H. ; Garrett, K.A. ; Andersen, K.F. ; Thomas-Sharma, S. ; Vlugt, R.A.A. van der - \ 2019
    Plant Pathology 68 (2019)8. - ISSN 0032-0862 - p. 1472 - 1480.
    farmer-multiplier - modelling - net tunnels - seed - sweet potato - virus-related degeneration

    Virus-related degeneration constrains production of quality sweet potato seed, especially under open field conditions. Once in the open, virus-indexed seed is prone to virus infection leading to decline in performance. Insect-proof net tunnels have been proven to reduce virus infection under researcher management. However, their effectiveness under farmer-multiplier management is not known. This study investigated the ability of net tunnels to reduce degeneration in sweet potato under farmer-multiplier management. Infection and degeneration were assessed for two cultivars, Kabode and Polista, grown in net tunnels and open fields at two sites with varying virus pressures. There was zero virus incidence at both sites during the first five generations. Sweet potato feathery mottle virus and sweet potato chlorotic stunt virus were present in the last three generations, occurring singly or in combination to form sweet potato virus disease. Virus infection increased successively, with higher incidences recorded at the high virus pressure site. Seed degeneration modelling illustrated that for both varieties, degeneration was reduced by the maintenance of vines under net tunnel conditions. The time series of likely degeneration based on a generic model of yield loss suggested that, under the conditions experienced during the experimental period, infection and losses within the net tunnels would be limited. By comparison, in the open field most of the yield could be lost after a small number of generations without the input of seed with lower disease incidence. Adopting the technology at the farmer-multiplier level can increase availability of clean seed, particularly in high virus pressure areas.

    Perceptions of integrated crop-livestock systems for sustainable intensification in the Brazilian Amazon
    Cortner, O. ; Garrett, R.D. ; Valentim, J.F. ; Ferreira, J. ; Niles, M.T. ; Reis, J. ; Gil, J. - \ 2019
    Land Use Policy 82 (2019). - ISSN 0264-8377 - p. 841 - 853.
    Farmer decision-making - Innovation - Integrated systems - Pasture intensification - Supply chains - Sustainable agriculture - Technology diffusion

    Sustainable intensification of existing global croplands and rangelands is a pressing challenge to reconcile competing demands on land systems for food production and conservation of natural ecosystems. In Brazil, the world's second-largest beef-producing country, intensification of pasture-based production systems is central to both improving livelihoods and reducing deforestation, since low-productivity, low-income cattle ranches occupy a majority of the agricultural land area. Integrated crop-livestock systems (ICLS) present a promising opportunity in the array of possible agricultural intensification strategies for Brazil because they have the potential to reclaim vast areas of degraded pastures while mitigating greenhouse gas emissions. Much of the previous research on ICLS, particularly in Brazil, has focused on agronomic and economic aspects. Here we examine local perspectives of ICLS to better illuminate what other concerns, besides agronomic and economic outcomes, might guide farmers’ decisions to adopt this (and other) agricultural intensification strategies. We are particularly interested in the degree to which structural factors interact with personal experiences to shape information and values and farmers’ understanding of the costs and benefits of adopting a new technology. Using semi-structured interviews with a diverse sample of producers in four states in the Brazilian Amazon, we find that existing adopters perceived ICLS as a beneficial strategy for increasing the economic value and competitiveness of their farm, while most non-adopters did not. Ranchers in particular perceived intensification as a necessity to maintain their livelihood amidst declining profits and increased environmental oversight. However, both adopters and non-adopters described numerous structural barriers that impeded greater adoption of ICLS in the region, including problems obtaining qualified labor, a lack of marketing options, poor infrastructure, an unsupportive regulatory environment, and in some regions, poorly drained soils. Furthermore, non-monetary motives, such as maintaining one's existing quality of life and traditions, often drove decisions regardless of expected profit-maximization pathways. This work underscores the need to employ a more diverse set of policy tools beyond credit subsidies to encourage adoption of sustainable intensification strategies, including education programs, payments for the ecosystem services, and improved transportation and supply chain infrastructure that can support intensification and help create a climate of innovation.

    Raising the Stakes: Cassava Seed Networks at Multiple Scales in Cambodia and Vietnam
    Delaquis, Erik ; Andersen, Kelsey F. ; Minato, Nami ; Cu, Thuy Thi Le ; Karssenberg, Maria Eleanor ; Sok, Sophearith ; Wyckhuys, Kris A.G. ; Newby, Jonathan C. ; Burra, Dharani Dhar ; Srean, Pao ; Phirun, Iv ; Le, Niem Duc ; Pham, Nhan Thi ; Garrett, Karen A. ; Almekinders, Conny J.M. ; Struik, Paul C. ; Haan, Stef de - \ 2018
    Frontiers in Sustainable Food Systems 2 (2018). - ISSN 2571-581X - 21 p.
    Cassava is one of the most important annual crops in Southeast Asia, and faces increasing seed borne pest and disease pressures. Despite this, cassava seed systems have received scant research attention. In a first analysis of Vietnamese and Cambodian cassava seed systems, we characterized existing cassava seed systems in 2016–2017 through a farmer survey based approach at both national and community scales, with particular focus on identifying seed system actors, planting material management, exchange mechanisms, geographies, and variety use, and performed a network analysis of detected seed movement at the provincial level. Despite their status as self-organized “informal” networks, the cassava seed systems used by farmers in Vietnam and Cambodia are complex, connected over multiple scales, and include links between geographically distant sites. Cassava planting material was exchanged through farmer seed systems, in which re-use of farm-saved supply and community-level exchanges dominated. At the national level, use of self-saved seed occurred in 47 and 64% of seed use cases in Cambodia and Vietnam, respectively. Movement within communes was prevalent, with 82 and 78% of seed provided to others being exchanged between family and acquaintances within the commune in Cambodia and Vietnam, respectively. Yet, meaningful proportions of seed flows, mediated mostly by traders, also formed inter-provincial and international exchange networks, with 20% of Cambodia's seed acquisitions imported from abroad, especially neighboring Vietnam and Thailand. Dedicated seed traders and local cassava collection points played important roles in the planting material distribution network at particular sites. Sales of planting material were important means of both acquiring and providing seed in both countries, and commercial sale was more prevalent in high-intensity than in low-intensity production sites. Considerable variability existed in local seed networks, depending on the intensity of production and integration with trader networks. Adapted innovations are needed to upgrade cassava seed systems in the face of emerging pests and diseases, taking into account and building on the strengths of the existing systems; including their social nature and ability to quickly and efficiently distribute planting materials at the regional level.
    Three pillars of sustainability in fisheries
    Asche, F. ; Garlock, Taryn M. ; Anderson, J.L. ; Bush, S.R. ; Smith, Martin D. ; Anderson, Christopher M. ; Chu, Jingjie ; Garrett, K.A. ; Lem, Audun ; Lorenzen, K. ; Oglend, Atle ; Tveteras, Sigbjorn ; Vannuccini, Stefania - \ 2018
    Proceedings of the National Academy of Sciences of the United States of America 115 (2018)44. - ISSN 0027-8424 - p. 11221 - 11225.
    seafood - sustainability - social - economic - environmental
    Sustainability of global fisheries is a growing concern. The United Nations has identified three pillars of sustainability: economic development, social development, and environmental protection. The fisheries literature suggests that there are two key trade-offs among these pillars of sustainability. First, poor ecological health of a fishery reduces economic profits for fishers, and second, economic profitability of individual fishers undermines the social objectives of fishing communities. Although recent research has shown that management can reconcile ecological and economic objectives, there are lingering concerns about achieving positive social outcomes. We examined trade-offs among the three pillars of sustainability by analyzing the Fishery Performance Indicators, a unique dataset that scores 121 distinct fishery systems worldwide on 68 metrics categorized by social, economic, or ecological outcomes. For each of the 121 fishery systems, we averaged the outcome measures to create overall scores for economic, ecological, and social performance. We analyzed the scores and found that they were positively associated in the full sample. We divided the data into subsamples that correspond to fisheries management systems with three categories of access—open access, access rights, and harvest rights—and performed a similar analysis. Our results show that economic, social, and ecological objectives are at worst independent and are mutually reinforcing in both types of managed fisheries. The implication is that rights-based management systems should not be rejected on the basis of potentially negative social outcomes; instead, social considerations should be addressed in the design of these systems.
    Tradeoffs in the quest for climate smart agricultural intensification in Mato Grosso, Brazil
    Gil, Juliana D.B. ; Garrett, Rachael D. ; Rotz, Alan ; Daioglou, Vassilis ; Valentim, Judson ; Pires, Gabrielle F. ; Costa, Marcos H. ; Lopes, Luciano ; Reis, Julio C. - \ 2018
    Environmental Research Letters 13 (2018)6. - ISSN 1748-9318
    climate scenarios - integrated crop-livestock systems - low carbon agriculture - pasture intensification - sustainability

    Low productivity cattle ranching, with its linkages to rural poverty, deforestation and greenhouse gas (GHG) emissions, remains one of the largest sustainability challenges in Brazil and has impacts worldwide. There is a nearly universal call to intensify extensive beef cattle production systems to spare land for crop production and nature and to meet Brazil's Intended Nationally Determined Contribution to reducing global climate change. However, different interventions aimed at the intensification of livestock systems in Brazil may involve substantial social and environmental tradeoffs. Here we examine these tradeoffs using a whole-farm model calibrated for the Brazilian agricultural frontier state of Mato Grosso, one of the largest soybean and beef cattle production regions in the world. Specifically, we compare the costs and benefits of a typical extensive, continuously grazed cattle system relative to a specialized soybean production system and two improved cattle management strategies (rotational grazing and integrated soybean-cattle) under different climate scenarios. We found clear tradeoffs in GHG and nitrogen emissions, climate resilience, and water and energy use across these systems. Relative to continuously grazed or rotationally grazed cattle systems, the integreated soybean-cattle system showed higher food production and lower GHG emissions per unit of human digestible protein, as well as increased resilience under climate change (both in terms of productivity and financial returns). All systems suffered productivity and profitability losses under severe climate change, highlighting the need for climate smart agricultural development strategies in the region. By underscoring the economic feasibility of improving the performance of cattle systems, and by quantifying the tradeoffs of each option, our results are useful for directing agricultural and climate policy.

    Stadium Coltan : artisanal mining, reforms and social change in eastern Democratic Republic of Congo
    Wakenge, Claude Iguma - \ 2017
    Wageningen University. Promotor(en): D.J.M. Hilhorst, co-promotor(en): K. Vlassenroot; J.G.R. Cuvelier. - Wageningen : Wageningen University - ISBN 9789463434560 - 210
    mining - conflict - economic sociology - cooperatives - reconstruction - poverty - rural sociology - workers - feedstocks - minerals - congo democratic republic - central africa - mijnbouw - conflict - economische sociologie - coöperaties - reconstructie - armoede - rurale sociologie - werkers - industriële grondstoffen - mineralen - democratische republiek kongo - centraal-afrika

    In the Democratic Republic of Congo (DRC), the mining sector has the potential to play a pivotal role in post-conflict reconstruction (World Bank, 2008), and artisanal mining sustains the livelihoods of millions people in the country (PACT, 2010). However, in the last 15 years, minerals from this artisanal mining have been ill-reputed. Eastern DRC has often been characterised by chronic instability and violent conflicts (Autesserre, 2010; Stearns, 2011) because it is widely believed that minerals in this region have attracted the greed of national and foreign armed groups, who benefit from the mining business.

    Although this ‘greed hypothesis’ has been criticised for its inconsistent performance in explaining resource-related conflicts (Le Billon, 2010; Ross, 2006), various national and international reform initiatives have gained momentum (Verbruggen et al., 2011). These initiatives aim to make the Congolese artisanal mining sector more transparent and to prevent ‘conflict minerals’ from entering the international market. In 2014, 13 reform initiatives—10 focusing on 3T (tantalum, tin and tungsten) and three on gold—were operational in eastern DRC (Cuvelier et al. 2014: 5). The implicit assumptions are that mining reforms will fully ‘clean’ artisanal mining of violence and corruption and that this will contribute to sustaining people’s livelihoods (Garrett and Mitchell, 2009: 12).

    This study investigated initiatives intended to ‘formalise’ artisanal mining in DRC—in other words, they aimed to bring mining under state control. The study especially focuses on the effects of one among these initiatives—the ITRI Tin Supply Chain Initiative (iTSCi)—on two groups of actors: miners (creuseurs) and middlemen (négociants). This thesis thus presents a fine-grained case study of the iTSCi. Designed by the International Tin Research Institute in 2009, iTSCi provides a means of determining the origin of 3T and documenting the trading chain for these minerals by ‘tagging and bagging’ the loads of 3T near miners’ shafts (at postes d’achat/selling points or buying stations), at counting offices (comptoirs) and in mineral depots, before the minerals are exported through the international market.

    This is a qualitative study undertaken at three coltan mining sites of northern Katanga: Kahendwa, Kisengo and Mai-Baridi. Coltan has been extracted at these sites since 2007. From March 2013 to September 2014, data were collected using participant observation of people’s practices (extraction/sale of coltan and various types of interactions between trading houses, cooperatives, mineworkers (creuseurs) and middlemen (négociants), as well as detailed in-depth interviews with creuseurs, négociants and their households. Data were also collected from the staff of mining cooperatives, trading houses, state authorities and civil servants—predominantly of the Service d’Assistance et d’Encadrement du Small-Scale Mining (SAESSCAM) and the Division des Mines. The last group of informants were a group of clandestine coltan négociants (known as hiboux—literally, ‘owls’), who were followed in the study.

    The purpose of this research is to study the micro-dynamics of changes after the reforms following the implementation of iTSCi. The study thus provides insights into how iTSCi is concretely implemented and how it has altered the organisation of mining and the trade of coltan. The study also aims to examine how this organisation affected creuseurs and négociants. The main research question of this study is as follows:

    How have initiatives to reform artisanal mining (iTSCi in particular) affected institutional change, how does this relate to changes in patterns of coltan production and trade, how were creuseurs and négociants affected by these changes, and how did these groups respond in the coltan mining areas of Kahendwa, Kisengo and Mai Baridi (northern Katanga) from 2009 to 2014?

    Analytically, the study adopted three main theoretical perspectives. First, an actor-oriented approach was taken, building on the premise that individual actors have the agency, knowledge and experience to reflect upon their situation and to respond to changes in their surrounding context (Giddens, 1984). Although the examined mining reforms consist predominantly of ‘ready-made’ techniques such as iTSCi’s ‘tagging and bagging’, analysing reforms with an actor orientation helps to highlight people’s reactions and responses. This includes how reform policies are applied in institutions (e.g. mining cooperatives), how they interact, how they are assigned meaning and how they are negotiated by social actors (Christoplos and Hilhorst, 2009).

    Second, the study builds on the sociology of economic life, which holds that economic action is a form of social action that is socially ‘embedded’, meaning that it is linked with or dependent on actions and institutions (such as social networks) that are noneconomic in content, goals and processes (Granovetter, 2005). This perspective facilitates the analysis of the livelihoods of négociants, including mechanisms of smuggling minerals into and beyond the mining areas where iTSCi is in force.

    Third, this thesis introduced the original concept of ‘enclaves of regulations’. These enclaves refer to the mining areas where iTSCi or other reforms are in force. This thesis has shown that, although these ‘enclaves’ appear to be ‘closed’ and insulated from the environment in terms of the locally applied rules for the mining and trading of minerals (e.g. ‘tagging and bagging’), in reality, such closure is not complete. This thesis has demonstrated that it would therefore be more appropriate to consider these ‘enclaves’ as semi-autonomous fields with porous boundaries.

    Apart from the introduction and the concluding chapters, this thesis is composed of five chapters. Chapter 2 explores the evolution of the mineral sector in the Katanga province. It analyses the history of mining, the initiation of artisanal mining and how the ongoing reforms have been informed by this history. In this chapter, it is shown that there is a long history of the organisation of mining in the Katangese province. The reforms therefore did not enter into a stage of anarchy, or an institutional void, but they added a layer to already existing forms of organisation.

    Chapter 3 focuses on mining cooperatives as newly introduced institutions aimed at governing the artisanal mining sites. Through a single case study, the chapter analyses how these cooperatives —especially the Coopérative des Artisanaux Miniers du Congo, CDMC—were introduced into the mining areas and how they interacted and blended with pre-existing miners’ organisations. This chapter demonstrates that cooperatives have been an emergent—rather than durable—solution in terms of representing the interests of artisanal miners.

    In Chapter 4, I provide a different perspective on ‘conflict minerals’. I thus introduce the notion of ‘reform conflicts’ to emphasise that, although ongoing reforms aim to sever the supposed linkages between the artisanal mining business and violent conflicts, these reforms have become a driving force behind the emergence of new conflicts over property rights and access to minerals.

    Chapter 5 is about livelihoods. It analyses how the reforms have influenced the livelihoods and socioeconomic position of négociants. This chapter also explores what kind of opportunities the reforms have offered to this group of mineral brokers often considered powerful in the mineral supply chain and explains what kind of constraints the négociants have confronted and why they have opted to diversify their livelihood portfolios. The chapter has shown that the reforms have affected this group of mineral brokers in different ways. Some négociants were well off, whereas others have been excluded from the mineral commodity chain. These findings contradict the widespread opinion that négociants are always abusive brokers in the mineral production and commodity chain.

    Chapter 6 analyses the responses of creuseurs and négociants to iTSCi. Although the mining sites where iTSCi is in force appear to be ‘enclaves of regulations’, I explore the strategies of creuseurs and négociants to bypass iTSCi and the reforms, especially around the coltan trade. This chapter demonstrates that coltan smuggling is a deeply rooted practice. Despite the reforms, smuggling continues in different forms.

    All of the elements highlighted above suggest that mining reforms have undergone a major shift, from addressing the initial problems associated with ‘conflict minerals’ to creating or reinforcing various types of problems, such as the influence of ‘big men’ in the mining business, coltan smuggling and the emergence of new conflicts over accessing minerals. This means that reform initiatives such as iTSCi should be based on knowledge about the actual situation. Thus, understanding and addressing these new types of problems calls for a comprehensive approach at both local and broader levels.

    Social and ecological analysis of commercial integrated crop livestock systems : Current knowledge and remaining uncertainty
    Garrett, R.D. ; Niles, M.T. ; Gil, J.D.B. ; Gaudin, A. ; Chaplin-Kramer, R. ; Assmann, A. ; Assmann, T.S. ; Brewer, K. ; Faccio Carvalho, P.C. de; Cortner, O. ; Dynes, R. ; Garbach, K. ; Kebreab, E. ; Mueller, N. ; Peterson, C. ; Reis, J.C. ; Snow, V. ; Valentim, J. - \ 2017
    Agricultural Systems 155 (2017). - ISSN 0308-521X - p. 136 - 146.
    Agroecology - Ecosystem services - Food systems - Mixed crop livestock - Sustainable agriculture

    Crops and livestock play a synergistic role in global food production and farmer livelihoods. Increasingly, however, crops and livestock are produced in isolation, particularly in farms operating at the commercial scale. It has been suggested that re-integrating crop and livestock systems at the field and farm level could help reduce the pollution associated with modern agricultural production and increase yields. Despite this potential, there has been no systematic review to assess remaining knowledge gaps in both the social and ecological dimensions of integrated crop and livestock systems (ICLS), particularly within commercial agricultural systems. Based on a multi-disciplinary workshop of international experts and additional literature review, we assess the current knowledge and remaining uncertainties about large-scale, commercial ICLS and identify the source of remaining knowledge gaps to establish priorities for future research. We find that much is understood about nutrient flows, soil quality, crop performance, and animal weight gain in commercial ICLS, but there is little knowledge about its spatial extent, animal behavior or welfare in ICLS, or the tradeoffs between biodiversity, pest and disease control, greenhouse gas (GHG) mitigation, and drought and heat tolerance in ICLS. There is some evidence regarding the economic outcomes in commercial ICLS and supply chain and policy barriers to adoption, but little understanding of broader social outcomes or cultural factors influencing adoption. Many of these knowledge gaps arise from a basic lack of data at both the field and system scales, which undermines both statistical analysis and modeling efforts. Future priorities for the international community of researchers investigating the tradeoffs and scalability of ICLS include: methods standardization to better facilitate international collaborations and comparisons, continued social organization for better data utilization and collaboration, meta-analyses to answer key questions from existing data, the establishment of long term experiments and surveys in key regions, a portal for citizen science, and more engagement with ICLS farmers.

    Policies for reintegrating crop and livestock systems : A comparative analysis
    Garrett, Rachael D. ; Niles, Meredith ; Dias Bernardes Gil, Juliana ; Dy, Philip ; Reis, Julio ; Valentim, Judson - \ 2017
    Sustainability 9 (2017)3. - ISSN 2071-1050 - 22 p.
    Agroecology - Brazil - New zealand - Sustainable agriculture - United states

    The reintegration of crop and livestock systems within the same land area has the potential to improve soil quality and reduce water and air pollution, while maintaining high yields and reducing risk. In this study, we characterize the degree to which federal policies in three major global food production regions that span a range of socioeconomic contexts, Brazil, New Zealand, and the United States, incentivize or disincentivize the use of integrated crop and livestock practices (ICLS). Our analysis indicates that Brazil and New Zealand have the most favorable policy environment for ICLS, while the United States provides the least favorable environment. The balance of policy incentives and disincentives across our three cases studies mirrors current patterns of ICLS usage. Brazil and New Zealand have both undergone a trend toward mixed crop livestock systems in recent years, while the United States has transitioned rapidly toward continuous crop and livestock production. If transitions to ICLS are desired, particularly in the United States, it will be necessary to change agricultural, trade, environmental, biofuels, and food safety policies that currently buffer farmers from risk, provide too few incentives for pollution reduction, and restrict the presence of animals in crop areas. It will also be necessary to invest more in research and development in all countries to identify the most profitable ICLS technologies in each region.

    Determinants of crop-livestock integration in Brazil : Evidence from the household and regional levels
    Dias Bernardes Gil, Juliana ; Garrett, R. ; Berger, T. - \ 2016
    Land Use Policy 59 (2016). - ISSN 0264-8377 - p. 557 - 568.
    Agricultural technology diffusion - Integrated systems - Land cover change - Pasture degradation - Sustainable intensification

    Integrated crop-livestock systems (iCL) are advocated as a promising strategy to increase agricultural production and rehabilitate degraded pastures while mitigating GHG emissions. Although iCL in Brazil has increased over the past few years, it still occupies a small share of the country's total agricultural area. We investigate the determinants of iCL occurrence in Mato Grosso state, a globally important producer of beef cattle and grains that has experienced rapid land cover change and environmental degradation in recent decades. Our analysis encompasses two typical cases of iCL in Mato Grosso (the rotation of soy followed by pasture, and soy followed by maize and pasture) as well as biophysical, socioeconomic, and institutional factors observable at the household and/or municipality levels that may influence the wide-scale occurrence of iCL. Evidence at both scales suggests that knowledge and supply chain infrastructure play an important role in early occurrence of iCL, as they are more common in regions closer to iCL research stations and processing facilities of grains and cattle. On average iCL adopters are more educated and have better access to technical assistance and sector information than specialized farmers or ranchers. Most iCLs are concentrated near established soy areas and greater similarity exists between municipalities with iCL and soy-dominant municipalities vs. pasture-dominant municipalities. Our findings reveal the importance of specific conditions for iCL occurrence and iCL promotion in livestock-dominant regions. Incentives targeted at ranchers are crucial for the achievement of the Brazilian Government's goal to restore degraded pastures through agricultural intensification.

    Seed degeneration in potato: the need for an integrated seed health strategy to mitigate the problem in developing countries
    Thomas-Sharma, S. ; Abdurahman, A.A. ; Ali, S. ; Andrade-Piedra, J.L. ; Bao, S. ; Charkowski, A.O. ; Crook, D. ; Kadian, M. ; Kromann, P. ; Struik, P.C. ; Torrance, L. ; Garrett, K.A. ; Forbes, G.A. - \ 2016
    Plant Pathology 65 (2016)1. - ISSN 0032-0862 - p. 3 - 16.
    Seed potato degeneration, the reduction in yield or quality caused by an accumulation of pathogens and pests in planting material due to successive cycles of vegetative propagation, has been a long-standing production challenge for potato growers around the world. In developed countries this problem has been overcome by general access to and frequent use of seed, produced by specialized growers, that has been certified to have pathogen and pest incidence below established thresholds, often referred to as certified seed. The success of certified seed in developed countries has concentrated the research and development agenda on the establishment of similar systems in developing countries. Despite these efforts, certified seed has had little penetration into the informal seed systems currently in place in most developing countries. Small-scale farmers in these countries continue to plant seed tubers acquired through the informal seed system, i.e. produced on-farm or acquired from neighbours or local markets. Informal seed tubers frequently have poor health status, leading to significant reductions in yield and/or market value. This review emphasizes the need to refocus management efforts in developing countries on improving the health status of seed tubers in the informal system by integrating disease resistance and on-farm management tools with strategic seed replacement. This ‘integrated seed health strategy’ can also prolong the good health status of plants derived from certified seed, which would otherwise be diminished due to potential rapid infection from neighbouring fields. Knowledge gaps, development challenges and impacts of this integrated seed health strategy are discussed.
    The rise and fall of CRISPRs - dynamics of spacer acquisition and loss
    Westra, E.R. ; Brouns, S.J.J. - \ 2012
    Molecular Microbiology 85 (2012)6. - ISSN 0950-382X - p. 1021 - 1025.
    immune-system - streptococcus-thermophilus - acquired-resistance - antiviral defense - escherichia-coli - seed sequence - cas systems - rna - dna - repeats
    Bacteria and Archaea are continuously exposed to mobile genetic elements (MGE), such as viruses and plasmids. MGEs may provide a selective advantage, may be neutral or may cause cell damage. To protect against invading DNA, prokaryotes utilize a number of defence systems, including the CRISPR/Cas system. CRISPR/Cas systems rely on integration of invader sequences (spacers) into CRISPR loci that act as a genetic memory of past invasions. Processed CRISPR transcripts are utilized as guides by Cas proteins to cleave complementary invader nucleic acids. In this issue, two groups report on spacer acquisition and turnover dynamics of CRISPR loci in a thermoacidophilic archeon and a pathogenic bacterium. Erdmann and Garrett demonstrate that three of the six CRISPR loci of Sulfolobus solfataricus rapidly acquire new spacer sequences from a conjugative plasmid present in a virus mixture. Intriguingly, two distinct mechanisms of spacer integration are utilized: leader adjacent and internal CRISPR spacer acquisition. Lopez-Sanchez and co-workers studied the type II system of Streptococcus agalactiae and observe heterogeneity in the bacterial population. A fraction of the population lost one or more anti-mobilome spacer sequences during its cultivation, allowing the transfer of a MGE in this subpopulation and a rapid response to altering selection pressures
    Climate Change in the High Andes:implications and adaptation strategies for small-scale farmers
    Perez, C. ; Nicklin, C. ; Dangles, O. ; Vanek, S. ; Sherwood, S.G. ; Halloy, S. ; Garrett, K.A. ; Forbes, G.A. - \ 2010
    The International Journal of Environmental, Cultural, Economic and Social Sustainability 6 (2010). - ISSN 1832-2077 - p. 71 - 88.
    Abstract: Global climate change represents a major threat to sustainable farming in the Andes. Farmers have used local ecological knowledge and intricate production systems to cope, adapt and reorganize to meet climate uncertainty and risk, which have always been a fact of life. Those traditional systems are generally highly resilient, but the predicted effects, rates and variability of climate change may push them beyond their range of adaptability. This article examines the extent of actual and potential impacts of climate variability and change on small-scale farmers in the highland Andes of Bolivia, Ecuador and Peru. It describes how climate change impacts agriculture through deglaciation, changes in hydrology, soil and pest and disease populations. The article highlights some promising adaptive strategies currently in use by or possible for producers, rural communities and local institutions to mitigate climate change effects while preserving the livelihoods and environmental and social sustainability of the region
    Assessing the impact of roads on animal population viability
    Grift, E.A. van der; Verboom, J. ; Pouwels, R. - \ 2003
    In: Making connections; international conference of ecology and transportation; 2003 proceedings. - Raleigh NC (USA) : Center for Transportation and the Environment - p. 173 - 181.
    Different tools have been developed to study the potential effects of spatial developments, such as the construction of roads, on the viability of animal populations. For instance, with dynamic (meta)population models the impacts of spatial developments can be accurately quantified. However, these models are often species specific and require detailed field research to validate the parameters used. If a multi-species analyses is needed, the use of such models is often impractical and expensive. In that case, an expert system, in which analyses of different species can be aggregated, may be a better tool to assess these kinds of impacts. Pros and cons of both types of tools are illustrated with (1) the ex-ante analyses of badger (Meles meles) population viability in central Limburg (The Netherlands) after the (proposed) construction of highway A73, and (2) the multi-species analyses of high priority locations to restore habitat connectivity across main roads in The Netherlands.
    Assessing the geographic representativeness of genebank collections: the case of Bolivian wild potatoes.
    Hijmans, R.J. ; Garrett, K.A. ; Huaman, Z. ; Zhang, D.P. ; Schreuder, M. ; Bonierbale, M. - \ 2000
    Conservation Biology 14 (2000)6. - ISSN 0888-8892 - p. 1755 - 1765.
    A BAC library and paired-PCR approach to mapping and completing the genome sequence of Sulfolobus solfataricus P2 : an EC perspective
    She, Q. ; Confalonieri, F. ; Zivanovic, Y. ; Medina, N. ; Billault, A. ; Awayez, M.J. ; Thi-Ghoc, H.P. ; Thi-Pham, B.T. ; Oost, J. van der; Duguet, M. ; Garrett, R.A. - \ 2000
    Dna sequence 11 (2000). - ISSN 1042-5179 - p. 183 - 136.
    Gene content and organization of a 281-kbp contig from the genome of the extremely thermophilic archaeon, Sulfolobus solfataricus P2
    Charlebois, R. ; Confalonieri, F. ; Curtis, B. ; Doolittle, W.F. ; Duguet, M. ; Erauso, G. ; Faguy, D. ; Gaasterland, T. ; Garrett, R.A. ; Gordon, P. ; Kozera, C. ; Medina, N. ; Oost, J. van der; Peng, X. ; Ragan, M. ; She, Q. ; Singh, R.K. - \ 2000
    Genome 43 (2000)1. - ISSN 0831-2796 - p. 116 - 136.
    The sequence of a 281-kbp contig from the crenarchaeote Sulfolobus solfataricus P2 was determined and analysed. Notable features in this region include 29 ribosomal protein genes, 12 tRNA genes (four of which contain archaeal-type introns), operons encoding enzymes of histidine biosynthesis, pyrimidine biosynthesis, and arginine biosynthesis, an ATPase operon, numerous genes for enzymes of lipopolysaccharide biosynthesis, and six insertion sequences. The content and organization of this contig are compared with sequences from crenarchaeotes, euryarchaeotes, bacteria, and eukaryotes.
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